What happens is Javascript hides or fades all questions with a .tagged-ignored' class, and highlights all questions with a .tagged-interesting` class. When a question has both classes, they overlap.

This is also why you will notice that when you hide ignored questions, you will have less questions on the entire page. Hiding the questions is taken over by javascript, not the server, so the server doesn't know to list more questions.

Not sure if this is the right place to feedback on this, but I find the "hide"/"ignore" feature detracts from the overall high quality of the site:

Because it's done browser-side, users see the ignored questions flashing up briefly and then the list of questions collapses in on itself, leaving huge amounts of empty space at the bottom of the page, with a variable number of remaining questions shown that doesn't agree with the number the user chose to prefer. So: A waste of some bandwidth and a hit to the aesthetics and consistency.

Not that it's a big priority, but I feel that at some point the "ignore" filtering should be moved to server side.